Before you ask about the delay of Book Two, consider the delay of Book One. Pat started The Kingkiller Chronicle in 1994. Back then, it was called The Song of Flame and Thunder (a title he'd later dismiss as "embarrassing"). It was "a hot mess":
I had no idea what I was doing in terms of structuring a story. I put words together fine. I could write dialog and scene. I could even make an interesting chapter. But a book is so much more than a series of interesting chapters. And that’s what it took me a fucking decade to figure out.
(Source: Interview with the Wired Book Club.)
Most of this revision went into Book One, though. Pat himself has said in the past that the book started to form when he stopped thinking of the trilogy as "the story" and started thinking of it as "the book."
So while Book One was revised, the 2007 drafts of Books Two and Three sucked. More on that below.
This led to revisions. And more revisions. And more and more revisions.